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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

Basic information

species Glycine max
transcript GLYMA11G14980.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gttagtttttttttttttaattt-gtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
|| || |||  |  || ||| ||  || || ||       | || |  ||| |   | |      ||  |   || ||||||    |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| ||||| ||||||||||||||||| |||||||| |||||||| || |||||
gtcagctttcctcattgtaacttcatgtttctgtaactccatgatc--cataattttaacacagcataatat-tggtcaattgc--cagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
    ||    ||  | || || | ||||||||||   |||  ||     | | || | | |        |  ||||||||| ||  ||| ||||||||||| || || ||||| || || |||||||| ||||| || ||||| || |||||||||||||| || || || ||||||||||| |||||
----gtaagcttgctattgatctatgattttgct---atatcaattttctaacagggttta--------taatgttcaattctt--agTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
gttagtttttttttttttaat-ttgtgatt--ttgctttgataggaacaacatgaaa-gtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
|| || ||||| ||  | ||  ||||  ||  || |||     | |      |     |  ||||   ||  |   ||   ||      |||| ||||||||||| |||||||| || || ||||||||||| |||||||| |||||||| ||||||||||| ||||||||||| ||||||||||| || ||
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgc--cagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
  ||    |   | |  |   ||||   |    ||||||       |    |||||  | |   ||  ||  ||||     ||  |||| ||||||||||| || |||||||| || ||||||||||| |||||||| ||||| |||||||||||||||||||| || || |||||||| || || ||
-gtaagcatcgctatcatgtcttgt--ctactatttgatc------atgccaaagttctga-caattctttttgttttgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 3
gttagtttttttttttttaat-ttgtgatt--ttgctttgataggaacaacatgaaa-gtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
|| || ||||| ||  | ||  ||||  ||  ||  |||    |     |  |     |  ||||   || ||   ||   || |    |||| ||| | ||||| | ||| || || || ||||||||||| |||||||| ||||||| |||||||||||| ||||||||||| ||||||||||| |||||
gtaagatttttattagtgaaagttgtatttatttagtttatccgctgttatgttttctgacatcatgcatattatttggggaaatgc--cagTTTATTCAGATGGGCTGGTGTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAGTGGTTATGAGCTCGCAAGTGAGCGTTGGACACCTGTGCATAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
|| || ||   | |        |||  |  ||  |        |  |  | |||||  | |   ||  ||  | ||     ||  |||| ||||| ||||| || |||||||| || ||||||||||| |||||||| ||||| | |||||||||||||||||| || || |||||||| || || ||
gtaagcttcactatc---ggactgtactcatgtctactatctgatcatgtcaaagttctga-caattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttc----aatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
||| ||| ||| |         |||| ||    |||||     || |   ||   ||    |  ||       ||||    |    || |||| ||||| ||||| || || |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||||||||||||  ||  | |||||
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC

upper sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gttagttttttttttttta-att--tgtgattttgctttgatagg-aacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
          | ||||   | |   |  | |  ||||| ||   |||  |     |     ||    |   ||      |       |     | |||||| ||||||||||| ||||||||||| |||||||| ||| |||||||||| |||||||||||||||||  | || |||||||| ||| | || || |||||
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|298167627|gb|HO012890.1|HO012890
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|208089572|gb|GD886161.1|GD886161
EST:     CACCTCAGAGTATTATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: CACCTCAGAG-A-TATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|298194743|gb|HO043215.1|HO043215
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|213587556|gb|DB969697.1|DB969697
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATC
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATC
EST: gi|14011884|gb|BG726806.1|BG726806
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|298182929|gb|HO028142.1|HO028142
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|298167833|gb|HO013096.1|HO013096
EST:     AAATAGTCCATCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTCGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|8286011|gb|BE023499.1|BE023499
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|208224042|gb|GE022585.1|GE022585
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|298183716|gb|HO028929.1|HO028929
EST:     AAATAGTCTACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGTCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|208061404|gb|GD859230.1|GD859230
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|298167168|gb|HO010607.1|HO010607
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGGTATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|16104747|gb|BI892487.1|BI892487
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|7284473|gb|AW597063.1|AW597063
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
EST: gi|213603235|gb|DB970406.1|DB970406
EST:     AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATG                         TATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG
genomic: AAATAGTCCACCTTCAGTGAAGTTCACCTCAGAGATATGGCACCCCAATGgttagttttt ... atttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC
 ctttgat  putative branch site (score: 5)
                                              tttttgc  putative PPT
                                         ttcaattttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA